BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 038945
         (363 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
 pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
          Length = 440

 Score = 28.9 bits (63), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 33/112 (29%), Positives = 51/112 (45%), Gaps = 14/112 (12%)

Query: 51  IENIKLSLFPRLKEIWHN----QALPVSFFN---NLRHLVLDDCKNMSSAIPANLIRCLN 103
           I N       +LKE+W      +++P   FN   +LR L L + K +S  I       L+
Sbjct: 127 IPNGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLS-YISEGAFEGLS 185

Query: 104 NLASLEVRNCD-----SLEEVLHLEELNADKEHLCPLFPKLFSLRLIDLPKL 150
           NL  L +  C+     +L  ++ L+EL+    HL  + P  F   L+ L KL
Sbjct: 186 NLRYLNLAMCNLREIPNLTPLIKLDELDLSGNHLSAIRPGSFQ-GLMHLQKL 236


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.322    0.137    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,322,728
Number of Sequences: 62578
Number of extensions: 347237
Number of successful extensions: 734
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 733
Number of HSP's gapped (non-prelim): 4
length of query: 363
length of database: 14,973,337
effective HSP length: 100
effective length of query: 263
effective length of database: 8,715,537
effective search space: 2292186231
effective search space used: 2292186231
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)